Merge pull request #70 from valentynbez/main

Release v1.1.2
bioinf-mcb · Feb 23, 2024 · 566037c · 566037c
2 parents ffbf60f + 40113db
commit 566037c
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,13 +13,7 @@ jobs:
     strategy:
       matrix:
         python-tag:
-        - cp38-manylinux_aarch64
-        - cp39-manylinux_aarch64
-        - cp310-manylinux_aarch64
         - cp311-manylinux_aarch64
-        - cp312-manylinux_aarch64
-        - pp38-manylinux_aarch64
-        - pp39-manylinux_aarch64
     steps:
     - uses: actions/checkout@v4
     - name: Set up QEMU
@@ -34,6 +28,7 @@ jobs:
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
@@ -48,13 +43,7 @@ jobs:
     strategy:
       matrix:
         python-tag:
-        - cp38-manylinux_x86_64
-        - cp39-manylinux_x86_64
-        - cp310-manylinux_x86_64
         - cp311-manylinux_x86_64
-        - cp312-manylinux_x86_64
-        - pp38-manylinux_x86_64
-        - pp39-manylinux_x86_64
     steps:
     - uses: actions/checkout@v4
     - name: Build manylinux wheels
@@ -64,6 +53,7 @@ jobs:
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
@@ -78,13 +68,7 @@ jobs:
     strategy:
       matrix:
         python-tag:
-        - cp38-macosx_x86_64
-        - cp39-macosx_x86_64
-        - cp310-macosx_x86_64
         - cp311-macosx_x86_64
-        - cp312-macosx_x86_64
-        - pp38-macosx_x86_64
-        - pp39-macosx_x86_64
     steps:
     - uses: actions/checkout@v4
     - name: Build manylinux wheels
@@ -94,6 +78,7 @@ jobs:
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
@@ -122,6 +107,7 @@ jobs:
         CIBW_BUILD: ${{ matrix.python-tag }}
         CIBW_BEFORE_BUILD: pip install cython
         CIBW_BUILD_VERBOSITY: 2
+        CIBW_TEST_COMMAND: python -m unittest mDeepFRI.tests -vv
         CIBW_TEST_REQUIRES: importlib-resources
       with:
         output-dir: dist
@@ -168,6 +154,8 @@ jobs:
       run: python -m pip install -U pip setuptools wheel
     - name: Install built wheel
       run: python -m pip install --no-binary mDeepFRI --find-links=dist mDeepFRI
+    - name: Run tests without coverage
+      run: python -m unittest mDeepFRI.tests -vv
 
   upload:
     environment: PyPI

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,8 +5,23 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+[Unreleased]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.2...HEAD
+
+## [v1.1.2] - 2024-02-22
+[v1.1.2]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.1.1...v1.1.2
+
+### Added
+- chunked loading of MMSeqs2 preselected targets - improves runtime
+
+### Fixed
+- C++17 lowered to C++14 for compatibility
+- pyopal API v0.5 integrated
+- removed `scipy` distance calculation with function
+- replaced `biopython` with `biotite` for structure manipulation - better runtime and easier deploy
+- tests fixed & added to CI/CD
 
 ## [v1.1.1] - 2024-03-01
+[v1.1.1]: https://github.com/bioinf-MCB/Metagenomic-DeepFRI/compare/v1.0.0...v1.1.1
 
 ### Added
 

diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 ## 🔍 Overview
 Proteins perform most of the work of living cells. Amino acid sequence and structural features of proteins determine a wide range of functions: from binding specificity and conferring mechanical stability, to catalysis of biochemical reactions, transport, and signal transduction.
 DeepFRI is a neural network designed to predict protein function within the framework of the Gene Ontology (GO). The exponential growth in the number of available protein sequences, driven by advancements in low-cost sequencing technologies and computational methods (e.g., gene prediction), has resulted in a pressing need for efficient software to facilitate the annotation of protein databases.
-Metagenomic-DeepFRI addresses such need, building upon efficient libraries. It incorporates novel databases of predicted structures (AlphaFold, ESM-Fold, MIP, etc.) and improves runtimes of DeepFRI by [2-12 times](https://github.com/bioinf-mcb/Metagenomic-DeepFRI/blob/main/weight_convert/onnx_vs_tf2.png)!
+Metagenomic-DeepFRI addresses such need, building upon efficient libraries. It incorporates novel databases of predicted structures (AlphaFold, ESMFold, MIP, etc.) and improves runtimes of DeepFRI by [2-12 times](https://github.com/bioinf-mcb/Metagenomic-DeepFRI/blob/main/weight_convert/onnx_vs_tf2.png)!
 
 ### 📋 Pipeline stages
 
@@ -33,9 +33,9 @@ cd Metagenomic-DeepFRI
 conda env create --name deepfri --file environment.yml
 conda activate deepfri
 ```
-3. Install `mDeepFRI`
+3. Show help message
 ```{code-block} bash
-pip install .
+mDeepFRI --help
 ```
 
 ## 💡 Usage

diff --git a/docs/source/usage.md b/docs/source/usage.md
@@ -54,7 +54,7 @@ Other available parameters can be found upon command `deepfri --help`.
    * - `--generate_contacts`
      - Gap fill during contact map alignment.
      - 2
-   * - `--mmseqs_min_bit_score`
+   * - `--mmseqs_min_bitscore`
      - Minimum bit score for MMSeqs2 search.
      - None
    * - `--mmseqs_max_evalue`
@@ -63,7 +63,7 @@ Other available parameters can be found upon command `deepfri --help`.
    * - `--mmseqs_min_identity`
      - Minimum sequence identity for MMSeqs2 search.
      - 0.5
-   * - `--mmseqs_min_bit_score`
+   * - `--mmseqs_min_bitscore`
      - Minimum bit score for MMSeqs2 search.
      - None
    * - `--threads`

diff --git a/environment.yml b/environment.yml
@@ -5,32 +5,16 @@ channels:
 dependencies:
   - click
   - numpy>=1.19
-  - scipy
-  - biopython
+  - biotite
   - mmseqs2=14.7e284
   - pip
-  - pytest
   - python==3.11
   - libdeflate
   - pip:
-    - pyopal
-    - pysam>=0.21.0
+    - pysam==0.21.0
+    - pyopal>=0.5
     - foldcomp
-    - cython
-    - requests
     # onnx stuff
-    - coloredlogs
-    - flatbuffers
-    - packaging
-    - protobuf
-    - sympy
-    - --extra-index-url https://aiinfra.pkgs.visualstudio.com/PublicPackages/_packaging/ORT-Nightly/pypi/simple/
-    - ort_nightly_gpu
-    - --extra-index-url=https://pypi.ngc.nvidia.com
-    - nvidia-cublas==11.5.1.101
-    - nvidia-cublas-cu117==11.10.1.25
-    - nvidia-cuda-runtime-cu114==11.4.148
-    - nvidia-cudnn==8.2.0.51
-    - nvidia-cudnn-cu11==8.5.0.96
-    - nvidia-cufft==10.4.2.58
-    - nvidia-curand==10.2.4.58
+    - onnxruntime-gpu
+    # mDeepFRI
+    - mdeepfri